nevermind! On windows I was running within eclipse. In linux I was running bins from a jar. I had renamed an old version of the jar, and didnt realize it would still look in this jar in the lib folder even though it had a different name. And this other jar file also had an xml conf file (by accident). On linux, it was apparently finding the conf file in this renamed jar and so it never looked in the "conf" folder for the most recent xml file.
subject: different behavior with regex on linux vs windows